Comparing performances of different statistical models and multiple threshold methods in a nested association mapping population of wheat.

Nested association mapping (NAM) populations emerged as a multi-parental strategy that combines the high statistical power of biparental linkage mapping with greater allelic richness of association mapping. Several statistical models have been developed for marker-trait associations (MTAs) in genome-wide association studies (GWAS), which ranges from simple to increasingly complex models. These statistical models vary in their performance for detecting real association with the avoidance of false positives and false negatives.

Association mapping reveals a reciprocal virulence/avirulence locus within diverse US Pyrenophora teres f. maculata isolates.

Background: Spot form net blotch (SFNB) caused by the necrotrophic fungal pathogen Pyrenophora teres f. maculata (Ptm) is an economically important disease of barley that also infects wheat. Using genetic analysis to characterize loci in Ptm genomes associated with virulence or avirulence is an important step to identify pathogen effectors that determine compatible (virulent) or incompatible (avirulent) interactions with cereal hosts.

Classification and Regression Models for Genomic Selection of Skewed Phenotypes: A Case for Disease Resistance in Winter Wheat ( L.).

Most genomic prediction models are linear regression models that assume continuous and normally distributed phenotypes, but responses to diseases such as stripe rust (caused by f. sp. tritici) are commonly recorded in ordinal scales and percentages.

Comparison of Single-Trait and Multi-Trait Genome-Wide Association Models and Inclusion of Correlated Traits in the Dissection of the Genetic Architecture of a Complex Trait in a Breeding Program.

Unknown genetic architecture makes it difficult to characterize the genetic basis of traits and associated molecular markers because of the complexity of small effect quantitative trait loci (QTLs), environmental effects, and difficulty in phenotyping. Seedling emergence of wheat ( L.) from deep planting, has a poorly understood genetic architecture, is a vital factor affecting stand establishment and grain yield, and is historically correlated with coleoptile length.

Comparison of genomic selection models for exploring predictive ability of complex traits in breeding programs.

Traits with a complex unknown genetic architecture are common in breeding programs. However, they pose a challenge for selection due to a combination of complex environmental and pleiotropic effects that impede the ability to create mapping populations to characterize the trait's genetic basis. One such trait, seedling emergence of wheat (Triticum aestivum L.

Why Are Black People Less Likely to Find a Stem Cell Donor Match?

Building trust in the health care system could increase the number of donors.

Breeding With Major and Minor Genes: Genomic Selection for Quantitative Disease Resistance.

Disease resistance in plants is mostly quantitative, with both major and minor genes controlling resistance. This research aimed to optimize genomic selection (GS) models for use in breeding programs that are needed to select both major and minor genes for resistance. In this study, stripe rust ( Westend.

Targeted management of influenza A/B outbreaks incorporating the cobas Influenza A/B & RSV into the virology laboratory.

During the 2017/18 influenza season, the authors' virology laboratory implemented the cobas Influenza A/B & RSV (Roche Molecular Diagnostics, Pleasanton, CA, USA) for influenza outbreak management in two scenarios: initial outbreak investigation or at outbreak conclusion to avoid prolonged measures. Twenty-seven investigations were conducted, including declaration of 11 influenza A/B outbreaks. Thirty percent of investigations would have missed the standard batched daily laboratory-developed respiratory polymerase chain reaction (PCR), and delayed outbreak confirmation until the following day.

HIV serology signal-to-cutoff ratio as a rapid method to predict confirmation of HIV infection.

Early and rapid detection of patients with HIV is a key to preventing further transmission. The purpose of this study was to assess the ability of signal-to-cutoff (S/CO) ratio from initial screening fourth-generation HIV serology to predict subsequent confirmation of HIV. Patients with a first-time positive HIV serology (S/CO ratio ≥ 1) from 2012 to 2016 were included.

Transitioning cytomegalovirus viral load testing from a laboratory developed test to the cobas CMV quantitative nucleic acid assay.

Commutability between human cytomegalovirus (CMV) viral load assays (VLA) is poor, despite the development of a WHO CMV International Standard (CMV IS). We evaluated a new CMV VLA, cobas CMV, as compared to our current laboratory developed CMV VLA (LDT), for clinical use. Both the LDT and cobas CMV were run in parallel for 109 patient samples.

Increase in Hospital Admissions for Severe Influenza A/B among Travelers on Cruise Ships to Alaska, 2015.

An increase in hospital admissions for influenza occurred during the summer of 2015 at an acute care facility in Vancouver, British Columbia, Canada. Investigation identified 25 patients with recent history of cruise ship travel to Alaska. All characterized influenza A viruses were A(H3N2).

A Large-Scale, Multiagency Approach to Defining a Reference Network for Pacific Northwest Streams.

Aquatic monitoring programs vary widely in objectives and design. However, each program faces the unifying challenge of assessing conditions and quantifying reasonable expectations for measured indicators. A common approach for setting resource expectations is to define reference conditions that represent areas of least human disturbance or most natural state of a resource characterized by the range of natural variability across a region of interest.

Implementation of Next-Generation Sequencing for Hepatitis B Virus Resistance Testing and Genotyping in a Clinical Microbiology Laboratory.

Sanger sequencing or DNA hybridization have been the primary modalities for hepatitis B (HBV) resistance testing and genotyping; however, there are limitations, such as low sensitivity and the inability to detect novel mutations. Next-generation sequencing (NGS) for HBV can overcome these limitations, but there is limited guidance for clinical microbiology laboratories to validate this novel technology. In this study, we describe an approach to implementing deep pyrosequencing for HBV resistance testing and genotyping in a clinical virology laboratory.

Does melatonin have therapeutic use in tinnitus?

Melatonin, a hormone produced by the pineal gland, may be a promising treatment option for tinnitus. The primary functions of this hormone are believed to be the initiation and maintenance of sleep because its secretions coincide with circadian rhythms. Some investigators have noted that melatonin may alleviate subjective symptoms of tinnitus.

Diffusion-weighted MR imaging of solid and cystic lesions of the pancreas.

Diffusion-weighted magnetic resonance (MR) imaging is increasingly used in the detection and characterization of pancreatic lesions. Diffusion-weighted imaging may provide additional information to radiologists evaluating patients who have cystic or solid neoplasms of the pancreas. Because of greater freedom of motion of water molecules in fluid-rich environments, simple cysts in the pancreas have higher signal intensity on diffusion-weighted images with a b value of 0 sec/mm2 and lower signal intensity on high-b-value images.

Diffusion-weighted MR imaging in pancreatic endocrine tumors correlated with histopathologic characteristics.

Purpose: To retrospectively assess apparent diffusion coefficients (ADCs) of different subtypes of pancreatic endocrine tumors based on the World Health Organization (WHO) classification system and analyze the potentially responsible histopathologic characteristics.

Materials And Methods: Following Institutional Review Board (IRB) approval, 18 patients with surgical pathology-proven pancreatic endocrine tumors were evaluated. Tumors were subcategorized based on the WHO grading classification into well-differentiated tumors with benign and uncertain behavior and endocrine carcinomas with well and poor differentiation.

Diffusion-weighted magnetic resonance imaging of pancreatic adenocarcinomas: association with histopathology and tumor grade.

Purpose: To evaluate the utility of diffusion-weighted magnetic resonance imaging (DWI) in pancreatic ductal adenocarcinoma with various grades of differentiation.

Materials And Methods: Following Institutional Review Board (IRB) approval, 21 consecutive patients with surgical pathology-proven pancreatic adenocarcinomas were retrospectively evaluated. Histopathologic characteristics and grades of differentiation of adenocarcinomas were analyzed.

MR imaging of hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is a common malignancy typically associated with chronic liver disease and is a leading cause of mortality among these patients. Prognosis is improved when detected early. MRI is the best imaging examination for accurate diagnosis.

Utility of diffusion-weighted MRI in distinguishing benign and malignant hepatic lesions.

Purpose: To evaluate apparent diffusion coefficient (ADC) values for characterization of a variety of focal liver lesions and specifically for differentiation of solid benign lesions (focal nodular hyperplasia [FNH] and adenomas) from solid malignant neoplasms (metastases and hepatocellular carcinoma [HCC]) in a large case series.

Materials And Methods: A total of 542 lesions in 382 patients were evaluated. ADC values were measured in 166 hemangiomas, 112 hepatomas, 107 metastases, 95 cysts, 10 abscesses, 43 FNH, and nine adenomas.

Utility of diffusion-weighted MRI in characterization of adrenal lesions.

Objective: The purpose of our study was to evaluate the utility of apparent diffusion coefficient (ADC) values for characterizing adrenal lesions and determine if diffusion-weighted imaging (DWI) can distinguish lipid-rich from lipid-poor adenomas.

Materials And Methods: We retrospectively evaluated 160 adrenal lesions in 156 patients (96 women and 60 men; mean age, 63 years). ADCs and signal intensity (SI) decrease on chemical shift imaging were measured in adrenal lesions with a wide variety of pathologies.

Use of Sno Strip filter-paper wicks for collection of genital-tract samples allows reproducible determination of human immunodeficiency virus type 1 (HIV-1) RNA viral load with a commercial HIV-1 viral load assay.

To assess the reproducibility of measurements of cervical and vaginal human immunodeficiency virus (HIV) viral load, 92 duplicate cervical and 88 duplicate vaginal samples were collected from 13 HIV-infected women using Sno Strip filter-paper wicks. RNA was eluted from the strips, extracted, and assayed using a modified protocol for the Roche Cobas Amplicor HIV-1 Monitor assay. Pearson's correlation coefficient (R), coefficient of determination (D), and Bland-Altman plots (BA) were used to compare paired log10-transformed viral loads.

Comprehensive comparison of the VERSANT HIV-1 RNA 3.0 (bDNA) and COBAS AMPLICOR HIV-1 MONITOR 1.5 assays on 1,000 clinical specimens.

Background: Plasma human immunodeficiency virus type 1 (HIV-1) RNA level is an important parameter for patient management, yet viral load assays from different manufacturers are not standardized.

Objectives And Study Design: In this study, we evaluated the concordance between test results obtained for 1,000 plasma specimens collected from HIV-1-infected individuals measured with the VERSANT HIV-1 RNA 3.0 assay (bDNA) and the COBAS AMPLICOR HIV-1 MONITOR 1.

Multicenter evaluation of the VERSANT hepatitis B virus DNA 3.0 assay.

The VERSANT hepatitis B virus (HBV) 3.0 Assay (branched DNA [bDNA]) (referred to herein as VERSANT 3.0) was evaluated at four external sites for analytical sensitivity, specificity, reproducibility, linearity of quantification, and limits of detection.

Genotypic and environmental effects on lupin seed composition.

Currently, white lupin (Lupinus albus L.) is gaining importance due to its high nitrogen fixation capability and potential in sustainable crop production systems. Even though research conducted in Australia, Chile, Germany, New Zealand, and Portugal has indicated lupin's positive potential as human and animal food, such information from Virginia and adjoining areas of the United States is not available.

Simple sequence repeats in watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai).

Simple sequence repeat length polymorphisms were utilized to examine genetic relatedness among accessions of watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai).